MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b0871 b2297 b2458 b2925 b2097 b3617 b0517 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b0822 b3709 b3161 b0112 b1727 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b3821 b1380 b1912 b1473 b0594   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372237 (mmol/gDw/h)
  Minimum Production Rate : 0.556937 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.378625
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.920348
  EX_pi_e : 2.029872
  EX_so4_e : 0.650673
  EX_k_e : 0.072658
  EX_fe2_e : 0.005978
  EX_mg2_e : 0.003229
  EX_ca2_e : 0.001937
  EX_cl_e : 0.001937
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 47.724824
  EX_co2_e : 26.146894
  EX_h_e : 8.227633
  EX_ac_e : 2.528110
  Auxiliary production reaction : 0.556937
  EX_pyr_e : 0.049601
  EX_alltn_e : 0.000417
  DM_5drib_c : 0.000250
  EX_glyclt_e : 0.000249
  DM_4crsol_c : 0.000083

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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